CSIRO Petrichor HPC Configuration
To run an nf-core pipeline at CSIRO Petrichor HPC, execute with -profile singularity,csiro_petrichor. This will download and launch the csiro_petrichor.config which has been pre-configured with a setup suitable for the CSIRO Petrichor HPC cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
Access to CSIRO Petrichor HPC
Please be aware that you will need to have an active CSIRO HPC User Account in order to use this infrastructure. If you need help getting started, please see the guide for new users.
Launch an nf-core pipeline on Petrichor
Prerequisites
Before running the pipeline you will need to load Nextflow and Singularity, both of which are globally installed modules. You can do this by running the commands below:
module purge
module load nextflow singularityCluster considerations
Before running an nf-core pipeline you will need to set your project code as a Slurm environment variable:
export SBATCH_ACCOUNT=OD-012345You can retrieve a list of projects your ident is associate with using:
get_project_codesExecution command
module load nextflow
module load singularity
nextflow run <nf-core_pipeline>/main.nf \
-profile singularity,csiro_petrichor \
<additional flags>Config file
// CSIRO Petrichor nf-core configuration profile
params {
config_profile_description = 'CSIRO Petrichor HPC profile provided by nf-core/configs'
config_profile_contact = 'Mitchell OBrien (@mitchob)'
config_profile_url = 'https://confluence.csiro.au/display/SC/CSIRO+SC+Shared+Cluster+-+Petrichor'
}
// Enable use of Singularity to run containers
singularity {
enabled = true
autoMounts = true
autoCleanUp = true
}
// Submit up to XX concurrent jobs
//executor {
// queueSize = XX
//}
// Define process resource limits
process {
executor = 'slurm'
clusterOptions = "--account=${System.getenv('SBATCH_ACCOUNT')}"
module = 'singularity/3.8.7'
cache = 'lenient'
stageInMode = 'symlink'
queue = 'defq'
}
executor
contact
